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- PDB-8a48: Less crystallisable" IgG1 Fc fragment (E382S variant) -

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Basic information

Entry
Database: PDB / ID: 8a48
TitleLess crystallisable" IgG1 Fc fragment (E382S variant)
ComponentsIgG1 Fc
KeywordsIMMUNE SYSTEM / Antibody / IgG / Fc / Fragment crystallisable
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.044 Å
AuthorsSudol, A.S.L. / Tews, I. / Crispin, M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2022
Title: Extensive substrate recognition by the streptococcal antibody-degrading enzymes IdeS and EndoS.
Authors: Sudol, A.S.L. / Butler, J. / Ivory, D.P. / Tews, I. / Crispin, M.
History
DepositionJun 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 11, 2023Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IgG1 Fc
B: IgG1 Fc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9625
Polymers51,1422
Non-polymers2,8203
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.780, 106.780, 104.011
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-511-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 237 - 443 / Label seq-ID: 17 - 223

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Antibody IgG1 Fc


Mass: 25570.982 Da / Num. of mol.: 2 / Mutation: E382S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFUSE-hIgG1-Fc / Cell line (production host): HEK 293-F / Production host: Homo sapiens (human)
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1463.349 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.25 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ammonium sulphate, 0.1 M Tris (pH 7.5), 25 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 18, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.04→47.543 Å / Num. obs: 13476 / % possible obs: 99.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.034 / Rrim(I) all: 0.048 / Net I/σ(I): 15.2
Reflection shellResolution: 3.04→3.25 Å / Rmerge(I) obs: 1.117 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2358 / Rpim(I) all: 1.117 / Rrim(I) all: 1.58 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AVE

3ave


Resolution: 3.044→47.543 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.181 / SU B: 50.271 / SU ML: 0.362 / Average fsc free: 0.9435 / Average fsc work: 0.9454 / Cross valid method: FREE R-VALUE / ESU R Free: 0.355
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2179 654 4.853 %
Rwork0.1966 12822 -
all0.198 --
obs-13476 99.682 %
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 136.227 Å2
Baniso -1Baniso -2Baniso -3
1-1.364 Å20.682 Å20 Å2
2--1.364 Å2-0 Å2
3----4.424 Å2
Refinement stepCycle: LAST / Resolution: 3.044→47.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3331 0 189 29 3549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0123631
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163204
X-RAY DIFFRACTIONr_angle_refined_deg0.7971.7074974
X-RAY DIFFRACTIONr_angle_other_deg0.3081.6347580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8395415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.323512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07510582
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.99910150
X-RAY DIFFRACTIONr_chiral_restr0.0390.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023965
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02644
X-RAY DIFFRACTIONr_nbd_refined0.1690.2548
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.22864
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21731
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21820
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.256
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.215
X-RAY DIFFRACTIONr_nbd_other0.1740.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0730.21
X-RAY DIFFRACTIONr_mcbond_it1.58610.5261666
X-RAY DIFFRACTIONr_mcbond_other1.58510.5261666
X-RAY DIFFRACTIONr_mcangle_it2.75515.7872079
X-RAY DIFFRACTIONr_mcangle_other2.75415.7892080
X-RAY DIFFRACTIONr_scbond_it1.5710.9881965
X-RAY DIFFRACTIONr_scbond_other1.56210.9771961
X-RAY DIFFRACTIONr_scangle_it2.78316.4152895
X-RAY DIFFRACTIONr_scangle_other2.77816.3992890
X-RAY DIFFRACTIONr_lrange_it7.004205.61513897
X-RAY DIFFRACTIONr_lrange_other7.001205.6113894
X-RAY DIFFRACTIONr_ncsr_local_group_10.1210.056106
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.120780.0501
12AX-RAY DIFFRACTIONLocal ncs0.120780.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.044-3.1220.46380.3918960.3949730.8150.82495.99180.389
3.122-3.2070.357420.3679100.3669520.8690.871000.365
3.207-3.30.315270.3458900.3449170.9110.8991000.34
3.3-3.4010.351530.338620.3329150.9050.9141000.312
3.401-3.5120.289430.2868120.2868550.9470.941000.266
3.512-3.6350.308450.2568190.2598640.9370.9571000.234
3.635-3.7710.276470.2427810.2448280.9370.9591000.218
3.771-3.9240.194300.2317630.2297930.9790.9661000.202
3.924-4.0970.235390.2017250.2037640.9640.9741000.181
4.097-4.2950.204340.186940.1827280.9730.981000.164
4.295-4.5260.176350.1696660.1697010.9860.9821000.153
4.526-4.7980.199360.1546190.1566550.9740.9851000.146
4.798-5.1250.148190.1586080.1586270.990.9841000.15
5.125-5.530.181500.1515350.1535850.980.9851000.145
5.53-6.050.223290.1675070.175360.9720.9821000.162
6.05-6.750.21300.1854670.1864970.9770.9781000.177
6.75-7.7690.267190.1824210.1854400.9510.9791000.19
7.769-9.4520.211160.1463670.1483830.9750.9861000.161
9.452-13.110.146130.1672930.1663060.9880.9831000.189
13.11-47.5430.26390.2561870.2561960.9620.9581000.292
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.15691.0896-1.1561.6648-0.94623.9140.0872-0.19950.53260.27960.05150.3454-0.3368-0.5286-0.13880.29840.1845-0.0880.2715-0.03990.246556.7034-20.94690.8806
24.585-0.51811.11751.61270.13182.18760.07710.27640.21840.0532-0.18290.05960.0467-0.11510.10580.2721-0.05940.01830.09520.0630.120851.5203-10.76-21.8581
Refinement TLS groupSelection: ALL

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